Longitudinal transcriptome analysis of cattle infected with Theileria parva

The apicomplexan cattle parasite Theileria parva is a major barrier to improving the livelihoods of smallholder farmers in Africa, killing over one million cattle on the continent each year. Although exotic breeds not native to Africa are highly susceptible to the disease, previous studies have illustrated that such breeds often show innate tolerance to infection by the parasite. The mechanisms underlying this tolerance remain largely unclear. To better understand the host response to T. parva infection we characterised the transcriptional response over 15 days in tolerant and susceptible cattle (n = 29) naturally exposed to the parasite. We identify key genes and pathways activated in response to infection as well as, importantly, several genes differentially expressed between the animals that ultimately survived or succumbed to infection. These include genes linked to key cell proliferation and infection pathways. Furthermore, we identify response expression quantitative trait loci containing genetic variants whose impact on the expression level of nearby genes changes in response to the infection. These therefore provide an indication of the genetic basis of differential host responses. Together these results provide a comprehensive analysis of the host transcriptional response to this under-studied pathogen, providing clues as to the mechanisms underlying natural tolerance to the disease.

Optical mapping compendium of structural variants across global cattle breeds

Structural variants (SV) have been linked to important bovine disease phenotypes, but due to the difficulty of their accurate detection with standard sequencing approaches, their role in shaping important traits across cattle breeds is largely unexplored. Optical mapping is an alternative approach for mapping SVs that has been shown to have higher sensitivity than DNA sequencing approaches. The aim of this project was to use optical mapping to develop a high-quality database of structural variation across cattle breeds from different geographical regions, to enable further study of SVs in cattle. To do this we generated 100X Bionano optical mapping data for 18 cattle of nine different ancestries, three continents and both cattle sub-species. In total we identified 13,457 SVs, of which 1,200 putatively overlap coding regions. This resource provides a high-quality set of optical mapping-based SV calls that can be used across studies, from validating DNA sequencing-based SV calls to prioritising candidate functional variants in genetic association studies and expanding our understanding of the role of SVs in cattle evolution.

Measurement(s)	Optical Mapping
Technology Type(s)	Optical Mapping
Factor Type(s)	Structural variants
Sample Characteristic - Organism	Bos taurus
Sample Characteristic - Location	United Kingdom • Kenya • Zambia • Uganda • Brazil • Nigeria

Seroprevalence of respiratory viral pathogens of indigenous calves in Western Kenya

Most studies of infectious diseases in East African cattle have concentrated on gastro-intestinal parasites and vector-borne diseases. As a result, relatively little is known about viral diseases, except for those that are clinically symptomatic or which affect international trade such as foot and mouth disease, bluetongue and epizootic haemorrhagic disease. Here, we investigate the seroprevalence, distribution and relationship between the viruses involved in respiratory disease, infectious bovine rhinotracheitis virus (IBR), bovine parainfluenza virus Type 3 (PIV3) and bovine viral diarrhoea virus (BVDV) in East African Shorthorn Zebu calves. These viruses contribute to the bovine respiratory disease complex (BRD) which is responsible for major economic losses in cattle from intensive farming systems as a result of pneumonia. We found that calves experience similar risks of infection for IBR, PIV3, and BVDV with a seroprevalence of 20.9%, 20.1% and 19.8% respectively. We confirm that positive associations exist between IBR, PIV3 and BVDV; being seropositive for any one of these three viruses means that an individual is more likely to be seropositive for the other two viruses than expected by chance.

Development and testing of a field diagnostic assay for peste des petits ruminants virus

We have developed an immunochromatographic test for the diagnosis of peste des petits ruminants (PPR) under field conditions. The diagnostic assay has been tested in the laboratory and also under field conditions in Ivory Coast, Pakistan, Ethiopia and Uganda. The test is carried out on a superficial swab sample (ocular or nasal) and showed a sensitivity of 84% relative to PCR. The specificity was 95% over all nasal and ocular samples. The test detected as little as 10³ TCID₅₀ (50% tissue culture infectious doses) of cell culture-grown virus, and detected virus isolates representing all four known genetic lineages of peste des petits ruminants virus. Virus could be detected in swabs from animals as early as 4 days post-infection, at a time when clinical signs were minimal. Feedback from field trials was uniformly positive, suggesting that this diagnostic tool may be useful for current efforts to control the spread of PPR.

An enzyme-linked immunosorbent assay for detection of Theileria parva antibodies in cattle using a recombinant polymorphic immunodominant molecule

Field and experimental bovine infection sera were used in immunoblots of sporozoite and schizont lysates of Theileria parva to identify candidate diagnostic antigens. Four parasite antigens of Mr 67,000 (p67), 85,000 (the polymorphic immunodominant molecule, PIM), 104,000 (p104), and 150,000 (p150) were selected for a more detailed analysis. The p67 and p104 antigens were present only in the sporozoite lysates, whereas PIM and p150 were found in both sporozoite and schizont lysates. The four antigens were expressed as recombinant fusion proteins and were compared with each other in an enzyme-linked immunosorbent assay (ELISA) and in the whole-schizont-based indirect fluorescent antibody test (IFAT) in terms of their ability to detect antibodies in sera of experimentally infected cattle. The PIM-based ELISA provided a higher degree of sensitivity and specificity than did the ELISA using the other three recombinant antigens or the IFAT. Further evaluation of the PIM-ELISA using experimental sera derived from cattle infected with different hemoparasites and field sera from endemic and nonendemic T. parva areas showed that the assay had a sensitivity of > 99% and a specificity of between 94% and 98%.

Specificity of a novel red blood cell agglutination assay ('SimpliRED') for HIV-1/HIV-2 infection

The specificity and ease of use of a novel red blood cell assay for detection of HIV-1/HIV-2 antibodies was evaluated on 125 blood donor samples in Nairobi. The specificity was estimated as > 99%. The assay correctly identified five positive samples in the population, and was easy and rapid to perform. The data confirm results obtained for the assay from other regions and suggest that the assay is suitable for detection of HIV-infected individuals by minimally equipped laboratories.

Identification of neutralization and diagnostic epitopes on PIM, the polymorphic immunodominant molecule of Theileria parva

The polymorphic immunodominant molecule (PIM) of Theileria parva is expressed by the schizont and sporozoite stages of the parasite. We have recently cloned the cDNA encoding the PIM antigen from two stocks of the parasite: the cattle-derived T. parva (Muguga) stock and a buffalo-derived stock. The cDNAs were used in transient-transfection assays to assess the reactivity of the antigen with monoclonal antibodies (MAb) previously raised against schizont-infected cells and used for parasite strain identification. We demonstrate that 19 of the 25 MAb are specific for PIM. Antibody reactivities with deletion mutants of a fusion protein containing PIM and Pepscan analysis of the Muguga version of the molecule with 13 of the MAb indicate that there are at least 10 different epitopes throughout the molecule. None of the MAb react with a tetrapeptide repeat present in the central region of the molecule, probably because of an inability of BALB/c mice to produce antibodies to this repeat. In contrast, sera from infected cattle react strongly with the repeat region, suggesting that this region alone may be useful as a diagnostic reagent. Previous studies showed that MAb to PIM inhibit sporozoite infectivity of bovine lymphocytes in vitro, which suggests that the antigen may be useful in immunizing cattle against T. parva infection. Pepscan analysis revealed that sera from infected cattle reacted with peptides recognized by the neutralizing MAb, as did sera from cattle inoculated with a PIM-containing recombinant protein. The latter sera did not, however, neutralize sporozoite infectivity in vitro. These results will be useful in exploiting the strain identification, diagnostic, and immunizing potentials of this family of antigens.

An assay for the identification of antigens recognized by cytotoxic T cells, based on transient transfection of COS cells

The studies reported here describe methodology permitting the direct identification of antigens recognized by cytotoxic T lymphocytes. We demonstrated that bovine alloreactive CTL can detect a bovine MHC molecule transiently expressed in a COS cell population in a standard microcytotoxicity assay. We then showed that alloreactive CTL can detect cells expressing the bovine class I MHC molecule in a population of cells transfected with the plasmid containing the corresponding gene plus 100-fold as many plasmids containing an irrelevant gene. In addition, the transiently transfected COS cells can specifically restimulate CTL as detected by a standard microcytotoxicity assay using the target cell line. Overall, the results suggest that COS cells could be employed for the direct screening of an antigen or antigen gene library by immune CTL.

Structure and sequence variation of the genes encoding the polymorphic, immunodominant molecule (PIM), an antigen of Theileria parva recognized by inhibitory monoclonal antibodies

The polymorphic, immunodominant molecule (PIM) of Theileria parva is the predominant antigen recognized by sera from infected cattle and by monoclonal antibodies (mAb) used to differentiate parasite strains. As such, the antigen is under consideration as a diagnostic antigen, and since the mAbs can neutralize sporozoite infectivity in vitro, in immunization experiments. Initial comparison of two PIM cDNA sequences suggested that the PIM genes consist of conserved 5' and 3' termini flanking a central variable region. We present further evidence, based on sequence analysis, supporting this general structure for the PIM genes. Evidence is also presented for a single copy of the PIM gene per haploid genome, implying that the different versions of PIM are encoded by distinct alleles. The central variable region of the PIM allele from the T. parva (Marikebuni) stock was found to contain 13 copies of the tetrapeptide repeat Gln-Pro-Glu-Pro. We also detected point mutations in the 5' and 3' termini of the PIM alleles, including regions recognized by the neutralizing and typing mAb. This contrasted with the high sequence conservation of the two introns of the genes, suggesting that the protein is undergoing rapid evolution. Sequence comparison of PIM genes from buffalo- and cattle-derived parasites supported earlier results that the parasites infecting buffaloes constitute a more heterogeneous population than those from cattle.

Selection of BoCD25 monoclonal antibodies by screening mouse L cells transfected with the bovine p55-interleukin-2 (IL-2) receptor gene

The bovine interleukin-2 receptor-alpha (IL-2R alpha) gene has been isolated and a rabbit antiserum against a fusion protein of the gene has been produced. However, the antiserum does not inhibit IL-2-dependent proliferation. Since a panel of monoclonal antibodies (mAb) to bovine activation antigens was available, we transfected the gene into mouse L fibroblasts, selected stable transfectants with the rabbit antiserum, and screened for antibodies that bound the transfected cells but not the untransfected cells. Three mAb were selected and all three precipitated a molecule of M(r) 55,000 (under reducing conditions) from activated cells, as expected from homology with mouse and human IL-2R alpha (CD25, Tac). One of the three mAb was a strong inhibitor of IL-2-dependent proliferation of bovine lymphocytes. Thus, the availability of transfected cells allowed us to establish quickly and unequivocally the antigenic specificity of a number of antibodies.

The influence of temperature and serum deprivation on the synthesis of heat-shock proteins and alpha and beta tubulin in promastigotes of Leishmania major

We have examined changes in the relative synthesis of individual proteins in promastigotes of Leishmania major subjected to decreasing serum levels in vitro. We observed increases in the relative synthesis of the putative heat-shock proteins of 82 and 70 kDa and of proteins of 79 and 41 kDa but decreases in the synthesis of proteins of 38 and 28 kDa. The relative synthesis of alpha-tubulin increased, whereas that of beta-tubulin decreased, in promastigotes subjected to decreased serum concentrations. This uncoordinated regulation of the synthesis of the tubulin proteins was not reflected as an alteration in the relative levels of the messenger RNA of the respective proteins. We have also studied changes in the synthesis of proteins in L. major promastigotes subjected to a temperature change from 26 degrees C to 34 degrees C. The results indicate that the synthesis of putative heat-shock proteins of 82, 70, 65, 41, 23 and 22 kDa increased when the parasites were incubated at the higher temperature, although these proteins were synthesised in detectable amounts at 26 degrees C. We could not detect differences between infective and non-infective promastigotes, separated by binding to peanut agglutinin, in the synthesis of individual proteins in response to increased temperature. These results were confirmed by densitometer analysis of autoradiographs of labelled promastigote proteins, and the relative changes in the synthesis of the two major heat-shock proteins, as well as alpha- and beta-tubulin, were estimated.